When you compile Qt Mobility from source, a feature file (mobility.prf) is copied into QTDIR/mkspecs/features (where QTDIR is the directory of the Qt installed that Qt Mobility was compiled for - which corresponds to the version of qmake you're using).

I'm assuming that if you install Qt Mobility from a package it puts the corresponding feature file in the right place.

It's possibly Qt Creator is doing something more, but that's my understanding of how things roll from the terminal.